T-box Riboswitch Annotation Database - TBDB - JZGQIGX1 from - Sporolactobacillus laevolacticus DSM 442

T-box riboswitch JZGQIGX1

Putative ILE (GAU) T-box riboswitch from Sporolactobacillus laevolacticus DSM 442

Source information

TBDB ID	JZGQIGX1
Host organism	Sporolactobacillus laevolacticus DSM 442
Model used	Class I
Predicted regulation	Transcriptional
T-box riboswitch genomic accession	AWTC01000002.1:158533-158256
Downstream protein description	isoleucyl-tRNA synthetase
Downstream protein ID	GenBank: EST13129.1
T-box riboswitch length
Specifier loop sequence	AAUCA
T-box 5'-UGGN-3' sequence	UGGU
Predicted specifier	AUC
Predicted tRNA family	ILE (GAU)
Found cognate tRNA	True
Alternative specifiers	None
Metagenome	False
Structural predictions	Full

Genomic Context

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Full T-box riboswitch FASTA sequence

>T-box Riboswitch Sequence JZGQIGX1 TTAAATACTATGATAGGGAAAGTACTCGCTGCAAGGTCGCTCAGCGAGCTGGGATGAGGTGTGAGCCCGGCGTGGACGGCAGCGAGAAAAATCACCCTTGAGTTCGGGTGTGAACGGTTCCGGATTGAATCCGGGCTAGTAATACCTGACGTTGATTCGCGTTAAGAAGACATTGAGTGGCAGATTTTTTTGCTATTAGGGTGGTACCGCGGTCCTTCCGTCCCTTTGGGATGGAAGGACCTTTTT

Predicted secondary structures

T-box riboswitch JZGQIGX1 Antiterminator ......((......((((......((((((.......(((.......((((((............)))))))))......))))))........))))...)).(((((((..............................))))))).(((......)))..................(((((....)))))....((((.......((((.....)))))))).....................

T-box riboswitch JZGQIGX1 Terminator ......((......((((......((((((.......(((.......((((((............)))))))))......))))))........))))...)).(((((((..............................))))))).(((......)))..................(((((....))))).................((((((((((((((...)))))))))))))).....

Specifier and tRNA predictions

Top specifier

Top predicted specifier: AUC
Top predicted tRNA family: ILE (GAU)

Best tRNA match for top specifier >ILE (GAU) tRNA from Sporolactobacillus laevolacticus DSM 442
GGGCCTGTAGCTCAGCTGGTTAGAGCGCACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTCCACTCAGGCCCACCA

Predicted tRNA structure (((((((..((((.........)))).(((((.......))))).....(((((.......))))))))))))....

Alternative specifier 1

Alternative 1 for predicted specifier: -
Alternative 1 for predicted tRNA family: -

Best tRNA match for alternative specifier 1 >TBDB tRNA pairing failed
tRNAscan-SE failed to find tRNA in host organism with anticodon matching predicted T-box specifier.

Predicted tRNA structure No tRNA structure predicted.

Alternative specifier 2

Alternative 2 for predicted specifier: -
Alternative 2 for predicted tRNA family: -

Best tRNA match for alternative specifier 2 >TBDB tRNA pairing failed
tRNAscan-SE failed to find tRNA in host organism with anticodon matching predicted T-box specifier.

Predicted tRNA structure No tRNA structure predicted.

Minimum Free Energy (MFE) Calculations

Folding MFE predictions

Antiterminator	ΔG° (kcal/mol)	-7.3
Terminator	ΔG° (kcal/mol	-27.7
	ΔΔG° (kcal/mol)

*Calculations performed using Vienna RNAeval at 37°C. More information available on methods avaialble on BioRXIV.

INFERNAL T-box riboswitch prediction output

Infernal prediction values

E-Value
Score	108.7
Bias	0.0
CM Accuracy	0.96

*More information about the meaning of these values can be found here.

T-box riboswitch structure prediction from input sequence

Feature	Length	Locus
Stem I		[7,103]
Stem II region
Stem III
Specifier region	-	[90,92]
T-box UGGN locus	-	[202,205]
Antiterminator		[198,225]
Terminator		[211,246]
All stems	-	[[7, 103], [105, 148], [150, 161], [180, 193], [198, 225]]

Input source sequence >AWTC01000002.1:158533-158256
TTAAATACTATGATAGGGAAAGTACTCGCTGCAAGGTCGCTCAGCGAGCTGGGATGAGGTGTGAGCCCGGCGTGGACGGCAGCGAGAAAAATCACCCTTGAGTTCGGGTGTGAACGGTTCCGGATTGAATCCGGGCTAGTAATACCTGACGTTGATTCGCGTTAAGAAGACATTGAGTGGCAGATTTTTTTGCTATTAGGGTGGTACCGCGGTCCTTCCGTCCCTTTGGGATGGAAGGACCTTTTT

INFERNAL output sequence >Infernal-AWTC01000002.1:158533-158256
UUAAAUACUAUGAUAGGG-AAAGUACUCGCUGCAAGGUCGCU-CAGCGAGCUGGGAUGAGGUGUGAgCCCGGCGUGGACgGCAGCGAGAAAAAUCACCCUUGAGU-UCGGGUGUGAACgguuccggauugaauccGGGCUAGUAAUACCUGACGUUGAUUCGCGUUA-AGAAGACAUUGAGUGGCAGAUU--------UUUUUGCUAUUAGGGUGGUACCGCGGU--CCU-UCCGUCCCUUUG

INFERNAL output structure - (Antiterminator) >Infernal-Structure-AWTC01000002.1:158533-158256
::::::<<------<<<<-------<<<<<<-------<<<--------<<<<<<___________.>>>>>>>>>---.-->>>>>>-------->>>>--->>,,<<<<<<<____................._________>>>>>>>,<<<______>>>,,,,,,,,,,,,,,,,,,,<<<<<<<________>>>>>>>,,,,<<<<-------<<<<<______>>>>>>>>>:::